The twins, Hafsa and Ilham had a conjoined abdomen and shared a common urinary tract and hip.
Abdullah Al-Rabeeah, the head of the team, said that the fifth, most critical stage in the operation had been a success and that the twins were in stable condition after the surgery, which took several hours.
Saudi King Abdullah bin Abdul Aziz had ordered the operation to be carried out at hospital in Riyadh, the report said.
Al-Rabeeah has already led 10 successful operations to separate conjoined twins.
The Saudi king has supported operations to separate conjoined twins from countries such as Egypt, Poland, Philippines and Malaysia.